IQ-TREE multicore version 1.6.12 for Linux 64-bit built Aug 15 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    fermat (AVX2, FMA3, 1009 GB RAM)
Command: ../../iqtree -s Pettalidae_4genes.raxml -sp pet_4genes.partitions.txt -pre Pettalidae_4genes.raxml -m TESTNEW -bb 1000 -alrt 1000
Seed:    522316 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Fri Aug 19 22:27:00 2022
Kernel:  AVX+FMA - 1 threads (128 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 128 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file pet_4genes.partitions.txt ...
Reading alignment file Pettalidae_4genes.raxml ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 124 sequences with 5141 columns, 1800 distinct patterns
1105 parsimony-informative, 530 singleton sites, 3506 constant sites
                                           Gap/Ambiguity  Composition  p-value
   1  Aoraki_crypta_MCZ_134654                     3.72%    passed     76.01%
   2  Aoraki_denticulata_denticulata_MCZ_134639   17.23%    failed      2.05%
   3  Aoraki_denticulata_denticulata_MCZ_134642    5.45%    passed     71.06%
   4  Aoraki_denticulata_denticulata_MCZ_134646   17.20%    failed      1.61%
   5  Aoraki_denticulata_denticulata_MCZ_134647   57.81%    failed      0.00%
   6  Aoraki_denticulata_denticulata_MCZ_134659   39.19%    passed     94.13%
   7  Aoraki_denticulata_major_MCZ_134644          3.48%    passed     88.47%
   8  Aoraki_denticulata_major_MCZ_35669          18.75%    failed      0.18%
   9  Aoraki_grandis_MCZ_134652                   25.11%    failed      0.00%
  10  Aoraki_granulosa_MCZ_134675                 16.71%    failed      2.96%
  11  Aoraki_granulosa_MCZ_134684                  2.94%    passed     61.76%
  12  Aoraki_healyi_MCZ_134638                     3.05%    passed     51.59%
  13  Aoraki_inerma_MCZ_134648                    25.11%    failed      0.00%
  14  Aoraki_longitarsa_CMNZ                      12.33%    failed      0.28%
  15  Aoraki_longitarsa_MCZ_134656_1              12.92%    failed      0.20%
  16  Aoraki_longitarsa_MCZ_134656_2              12.33%    failed      0.28%
  17  Aoraki_longitarsa_MCZ_35659                  3.23%    passed     94.24%
  18  Aoraki_longitarsa_MCZ_35660                 12.35%    failed      0.26%
  19  Aoraki_tumidata_MCZ_133838                  14.18%    failed      0.46%
  20  Aoraki_westlandica_MCZ_134653                3.58%    passed     91.42%
  21  Archaeopurcellia_eureka_MCZ_162243          44.68%    failed      0.00%
  22  Archaeopurcellia_eureka_MCZ_162249          16.81%    passed     27.06%
  23  Austropurcellia_acuta_MCZ_134701             3.07%    passed     79.69%
  24  Austropurcellia_arcticosa_MCZ_132325        14.57%    passed     10.54%
  25  Austropurcellia_cadens_CASENT9035046        13.21%    failed      0.97%
  26  Austropurcellia_clousei_MCZ_132339           5.04%    passed     81.68%
  27  Austropurcellia_culminis_MCZ_132322          4.14%    passed     41.38%
  28  Austropurcellia_daviesae_MCZ_132323         13.17%    failed      2.24%
  29  Austropurcellia_despectata_MCZ_132324        3.75%    passed     71.29%
  30  Austropurcellia_giribeti_MCZ_132337          4.96%    passed     22.76%
  31  Austropurcellia_giribeti_MCZ_134696         12.37%    failed      1.18%
  32  Austropurcellia_scoparia_MCZ_134700          8.34%    passed     87.46%
  33  Austropurcellia_sharmai_MCZ_134698           3.00%    passed     44.80%
  34  Austropurcellia_tholei_MCZ_134697           12.37%    failed      4.99%
  35  Austropurcellia_vicina_MCZ_132318            3.99%    passed     15.78%
  36  Austropurcellia_vicina_MCZ_132334           13.21%    passed      6.08%
  37  Chileogovea_jocasta_MCZ_134713               5.60%    passed     81.53%
  38  Chileogovea_jocasta_MCZ_134714               3.05%    passed     50.93%
  39  Chileogovea_jocasta_MCZ_134715               3.09%    passed     45.95%
  40  Chileogovea_oedipus_MCZ_134709               3.09%    passed     51.30%
  41  Chileogovea_oedipus_MCZ_134710               3.09%    passed     49.44%
  42  Chileogovea_oedipus_MCZ_134711               7.70%    passed      5.73%
  43  Chileogovea_oedipus_MCZ_134712               3.07%    passed     50.23%
  44  Cyphophthalmus_duricorius_MCZ_135009        19.16%    failed      0.05%
  45  Karripurcellia_harveyi_MCZ_132345            2.90%    passed     34.50%
  46  Karripurcellia_peckorum_MCZ_134719           2.88%    passed     35.32%
  47  Karripurcellia_peckorum_MCZ_134720           4.03%    passed     58.74%
  48  Karripurcellia_peckorum_MCZ_134721           3.50%    passed     47.95%
  49  Karripurcellia_peckorum_MCZ_134725          12.37%    passed     12.30%
  50  Karripurcellia_peckorum_MCZ_134726          12.37%    passed     10.36%
  51  Limulus_polyphemus                           3.60%    passed     40.13%
  52  Metasiro_savannahensis                       4.67%    passed     91.10%
  53  Neopurcellia_salmoni_MCZ_133839             46.66%    failed      0.22%
  54  Neopurcellia_salmoni_MCZ_134739             21.86%    failed      0.50%
  55  Neopurcellia_salmoni_MCZ_134741              3.13%    passed     73.77%
  56  Neopurcellia_salmoni_MCZ_29317               3.15%    passed     74.16%
  57  Paramiopsalis_ramulosus_MCZ_135006           3.48%    passed     68.87%
  58  Parapurcellia_amatola_MCZ_133841            15.70%    failed      0.65%
  59  Parapurcellia_convexa_MCZ_128902             2.92%    passed     95.18%
  60  Parapurcellia_convexa_MCZ_134744             2.92%    passed     92.37%
  61  Parapurcellia_fissa_MCZ_134745               2.96%    passed     98.18%
  62  Parapurcellia_minuta_MCZ_134747              2.92%    passed     99.44%
  63  Parapurcellia_monticola_MCZ_134751          25.03%    failed      0.00%
  64  Parapurcellia_monticola_MCZ_60357_1         12.33%    failed      0.10%
  65  Parapurcellia_monticola_MCZ_60357_2         12.35%    failed      0.11%
  66  Parapurcellia_peregrinator_MCZ_128901       12.16%    failed      1.11%
  67  Parapurcellia_rumpiana_MCZ_134748            2.96%    passed     48.43%
  68  Parapurcellia_silvicola_MCZ_134742_1         2.90%    passed     95.47%
  69  Parapurcellia_silvicola_MCZ_134742_2         2.96%    passed     95.53%
  70  Parapurcellia_sp_MCZ_128900                 21.18%    failed      3.33%
  71  Parapurcellia_staregai_MCZ_134746            2.92%    passed     96.65%
  72  Parasiro_coiffaiti_MCZ_132372                4.71%    failed      2.01%
  73  Parasiro_minor_MCZ_132374                    3.13%    passed     17.30%
  74  Pettalus_sp_MCZ_132353                       2.84%    passed     67.27%
  75  Pettalus_sp_MCZ_132354                       2.80%    passed     34.22%
  76  Pettalus_sp_MCZ_132356                      12.39%    passed      5.62%
  77  Pettalus_sp_MCZ_132357                       2.96%    passed     80.11%
  78  Pettalus_sp_MCZ_132359                       2.80%    passed     37.75%
  79  Pettalus_sp_MCZ_132360                       2.94%    passed     78.19%
  80  Pettalus_sp_MCZ_134967                      15.06%    failed      0.59%
  81  Pettalus_thwaitesi_MCZ_132348                2.84%    passed     52.35%
  82  Purcellia_argasiformis_MCZ_134759            3.00%    passed     18.55%
  83  Purcellia_argasiformis_MCZ_134762            3.09%    passed     19.92%
  84  Purcellia_griswoldi_MCZ_128898              12.37%    passed     11.63%
  85  Purcellia_griswoldi_MCZ_134756               2.74%    passed     15.11%
  86  Purcellia_illustrans_MCZ_128896             12.37%    passed     15.24%
  87  Purcellia_illustrans_MCZ_134753             15.23%    passed     46.07%
  88  Purcellia_illustrans_MCZ_134754             12.37%    passed     18.43%
  89  Purcellia_illustrans_MCZ_60635               3.01%    passed     23.49%
  90  Purcellia_leleupi_MCZ_129098                 2.84%    passed     29.44%
  91  Purcellia_sp_MCZ_128897                      3.54%    passed     24.20%
  92  Purcellia_sp_MCZ_129493                      2.84%    passed     12.21%
  93  Purcellia_sp_MCZ_129494                      3.01%    passed     24.93%
  94  Rakaia_antipodiana_MCZ_134580                3.23%    passed     33.36%
  95  Rakaia_australis_MCZ_134592                  4.55%    passed     57.35%
  96  Rakaia_collaris_MCZ_134574                   4.34%    passed     89.14%
  97  Rakaia_digitata_MCZ_134571                   5.23%    passed     99.30%
  98  Rakaia_dorothea_MCZ_134577                   4.12%    passed     95.44%
  99  Rakaia_florensis_MCZ_134588                  3.03%    passed     69.96%
 100  Rakaia_lindsayi_MCZ_134598                  15.79%    failed      3.18%
 101  Rakaia_macra_MCZ_134582                      4.07%    passed     62.18%
 102  Rakaia_media_MCZ_134581                      3.13%    passed     45.34%
 103  Rakaia_media_MCZ_134605                      4.90%    passed     31.88%
 104  Rakaia_minutissima_MCZ_134591                3.25%    passed     62.96%
 105  Rakaia_minutissima_MCZ_29280                12.04%    passed     16.87%
 106  Rakaia_pauli_MCZ_134576                     10.95%    passed     77.13%
 107  Rakaia_solitaria_MCZ_134585                  3.07%    passed     31.76%
 108  Rakaia_sorenseni_MCZ_134567                  3.21%    passed     50.76%
 109  Rakaia_sp_MCZ_100753                         3.11%    passed     45.95%
 110  Rakaia_sp_MCZ_129612                         3.17%    passed     59.16%
 111  Rakaia_sp_MCZ_129614                         3.19%    passed     51.13%
 112  Rakaia_sp_MCZ_133847                         3.70%    passed     78.11%
 113  Rakaia_sp_MCZ_133849                         3.17%    passed     47.86%
 114  Rakaia_sp_MCZ_134568                        41.08%    failed      0.00%
 115  Rakaia_sp_MCZ_134575                         4.59%    passed     68.22%
 116  Rakaia_sp_MCZ_134584                         3.73%    passed     72.79%
 117  Rakaia_sp_MCZ_35662                          3.11%    passed     61.39%
 118  Rakaia_sp_MCZ_35668                          3.15%    passed     73.54%
 119  Rakaia_stewartiensis_MCZ_134599              4.07%    passed     52.61%
 120  Rakaia_uniloca_MCZ_134583                   12.88%    failed      1.98%
 121  Rakaia_uniloca_MCZ_134600                   25.13%    failed      0.00%
 122  Siro_exilis_MCZ_134551                      13.81%    failed      0.00%
 123  Siro_rubens_MCZ_132391                      12.70%    failed      1.43%
 124  Suzukielus_sauteri_MCZ_132256                3.38%    passed     57.46%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL                                        9.16%  34 sequences failed composition chi2 test (p-value<5%; df=3)

Partition file is not in NEXUS format, assuming RAxML-style partition file...
Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1	DNA	95	564	359	138	GTR	16S
2	DNA	122	1763	66	1565	GTR	18S
3	DNA	122	2157	276	1607	GTR	28S
4	DNA	112	655	404	196	GTR	COI
Degree of missing data: 0.050
Info: multi-threading strategy over partitions



Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.033 seconds
NOTE: ModelFinder requires 73 MB RAM!
Testing GTR+F+G on supermatrix...
GTR+F+G4 / LnL: -60107.646 / df: 254 / AIC: 120723.292 / AICc: 120749.816 / BIC: 122385.624
Selecting individual models for 4 charsets using BIC...
 No. Model        Score       Charset
   1 GTR+F+I+G4   34223.054   16S
   2 TNe+R2       10546.584   18S
   3 GTR+F+R6     21456.786   28S
   4 GTR+F+I+G4   50346.438   COI
Full partition model BIC score: 117970.960 (LnL: -55003.690  df:932)
Partition information was printed to Pettalidae_4genes.raxml.best_scheme.nex
Partition information in Raxml format was printed to Pettalidae_4genes.raxml.best_scheme

All model information printed to Pettalidae_4genes.raxml.model.gz
CPU time for ModelFinder: 301.344 seconds (0h:5m:1s)
Wall-clock time for ModelFinder: 302.387 seconds (0h:5m:2s)
Generating 1000 samples for ultrafast bootstrap (seed: 522316)...

NOTE: 36 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing GTR+F+R6 parameters for partition 28S (259 free parameters)
Optimizing GTR+F+I+G4 parameters for partition COI (231 free parameters)
Optimizing GTR+F+I+G4 parameters for partition 16S (197 free parameters)
Optimizing TNe+R2 parameters for partition 18S (245 free parameters)
Optimal log-likelihood: -55006.995
Computing ML distances based on estimated model parameters... 0.328 sec
WARNING: Some pairwise ML distances are too long (saturated)
Computing BIONJ tree...
0.032 seconds
Log-likelihood of BIONJ tree: -56772.882
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 3.814 second
Computing log-likelihood of 98 initial trees ... 10.805 seconds
Current best score: -54962.986

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -54851.743
Iteration 10 / LogL: -54894.725 / Time: 0h:1m:2s
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -54847.327
Iteration 20 / LogL: -54892.480 / Time: 0h:1m:15s
Finish initializing candidate tree set (19)
Current best tree score: -54847.327 / CPU time: 40.825
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 21: -54846.914
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -54845.404
Iteration 30 / LogL: -54848.176 / Time: 0h:1m:33s (0h:5m:1s left)
Iteration 40 / LogL: -54849.058 / Time: 0h:1m:48s (0h:3m:54s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 48: -54844.692
Iteration 50 / LogL: -54844.696 / Time: 0h:2m:5s (0h:4m:10s left)
Log-likelihood cutoff on original alignment: -54924.279
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -54844.418
Iteration 60 / LogL: -54867.003 / Time: 0h:2m:22s (0h:3m:56s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 67: -54842.844
Iteration 70 / LogL: -54870.365 / Time: 0h:2m:39s (0h:3m:44s left)
Iteration 80 / LogL: -54894.325 / Time: 0h:2m:55s (0h:3m:13s left)
Iteration 90 / LogL: -55101.254 / Time: 0h:3m:11s (0h:2m:46s left)
Iteration 100 / LogL: -54847.054 / Time: 0h:3m:28s (0h:2m:20s left)
Log-likelihood cutoff on original alignment: -54924.279
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 103: -54842.406
Iteration 110 / LogL: -54856.634 / Time: 0h:3m:45s (0h:3m:12s left)
Iteration 120 / LogL: -54876.491 / Time: 0h:4m:1s (0h:2m:48s left)
Iteration 130 / LogL: -54847.077 / Time: 0h:4m:17s (0h:2m:25s left)
Iteration 140 / LogL: -54846.741 / Time: 0h:4m:33s (0h:2m:3s left)
Iteration 150 / LogL: -55107.088 / Time: 0h:4m:49s (0h:1m:43s left)
Log-likelihood cutoff on original alignment: -54924.279
Iteration 160 / LogL: -54892.428 / Time: 0h:5m:7s (0h:1m:23s left)
Iteration 170 / LogL: -54846.305 / Time: 0h:5m:24s (0h:1m:3s left)
Iteration 180 / LogL: -54842.521 / Time: 0h:5m:41s (0h:0m:43s left)
Iteration 190 / LogL: -54845.349 / Time: 0h:5m:57s (0h:0m:24s left)
Iteration 200 / LogL: -54846.251 / Time: 0h:6m:12s (0h:0m:5s left)
Log-likelihood cutoff on original alignment: -54924.279
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
TREE SEARCH COMPLETED AFTER 204 ITERATIONS / Time: 0h:6m:19s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Optimizing GTR+F+R6 parameters for partition 28S (259 free parameters)
Optimizing GTR+F+I+G4 parameters for partition COI (231 free parameters)
Optimizing GTR+F+I+G4 parameters for partition 16S (197 free parameters)
Optimizing TNe+R2 parameters for partition 18S (245 free parameters)
Optimal log-likelihood: -54842.365
BEST SCORE FOUND : -54842.365

Testing tree branches by SH-like aLRT with 1000 replicates...
11.906 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Pettalidae_4genes.raxml.splits.nex
Total tree length: 5.900

Total number of iterations: 204
CPU time used for tree search: 342.696 sec (0h:5m:42s)
Wall-clock time used for tree search: 344.775 sec (0h:5m:44s)
Total CPU time used: 391.880 sec (0h:6m:31s)
Total wall-clock time used: 394.271 sec (0h:6m:34s)

Computing bootstrap consensus tree...
Reading input file Pettalidae_4genes.raxml.splits.nex...
124 taxa and 514 splits.
Consensus tree written to Pettalidae_4genes.raxml.contree
Reading input trees file Pettalidae_4genes.raxml.contree
Log-likelihood of consensus tree: -54841.969

Analysis results written to: 
  IQ-TREE report:                Pettalidae_4genes.raxml.iqtree
  Maximum-likelihood tree:       Pettalidae_4genes.raxml.treefile
  Likelihood distances:          Pettalidae_4genes.raxml.mldist
  Best partitioning scheme:      Pettalidae_4genes.raxml.best_scheme.nex
           in RAxML format:      Pettalidae_4genes.raxml.best_scheme

Ultrafast bootstrap approximation results written to:
  Split support values:          Pettalidae_4genes.raxml.splits.nex
  Consensus tree:                Pettalidae_4genes.raxml.contree
  Screen log file:               Pettalidae_4genes.raxml.log

Date and Time: Fri Aug 19 22:38:38 2022
